Objective To investigate the impact of depth of bowel wall invasion on clinical characteristics and prognosis in ovarian cancer patients with intestinal metastasis undergoing bowel resection. Methods A retrospective analysis was conducted on 65 patients with epithelial ovarian cancer who underwent cytoreductive surgery combined with bowel resection at Shanghai Ruijin Hospital from October 2013 to March 2025. Patients were divided into two groups according to the depth of bowel wall invasion: the serosa/muscularis invasion group (n=47) and the mucosa/submucosa invasion group (n=18). Clinicopathological characteristics and progression-free survival (PFS) were compared between the two groups. Results The median PFS was significantly longer in the mucosa/submucosa invasion group than in the serosa/muscularis invasion group (51.6 months vs. 27.2 months, P=0.014). Compared with the serosa/muscularis invasion group, the mucosa/submucosa invasion group had lower serum CA125 levels at initial diagnosis (300.5 U/mL vs. 1 050.0 U/mL, P=0.034), a higher rate of preoperative imaging detection of intestinal metastasis (100% vs. 48.9%, P<0.001), a lower proportion of patients with massive ascites at initial diagnosis (11.1% vs. 48.9%, P=0.005), and the intraoperative peritoneal cancer index (PCI) was also lower (8.7±4.6 vs. 13.4±6.5, P=0.007). No statistically significant differences were observed between the two groups in terms of surgery-related indicators and perioperative complications (all P>0.05). Conclusions In patients with ovarian cancer intestinal metastasis undergoing bowel resection, depth of bowel wall invasion is closely associated with prognosis. Those with invasion reaching the mucosa/submucosa have better prognosis and a relatively weak ability for abdominopelvic seeding. Thus, precise preoperative assessment of invasion depth may help optimize surgical strategies.